If the saves used to break encryption (save1, save2, save3, a.k.a. 26.sav, 16.sav, 165.sav) contain Pokemon in boxes other than 1 and 2, decryption of some slots fails, resulting in no Pokemon listed in a slot where there is Pokemon, and listing <100% Pokemon in slots that are empty.
For example, if I break encryption using three saves that contain ONLY the six Pokemon in the proper spots in the first two boxes, then I open saves that are empty, full1, and full2, decryption is fully successful. When I then re-open empty, no Pokemon appear, and when I re-open full1 or full2, all 930 Pokemon appear with no ~ markers. This is correct behavior.
However, if I break encryption using three saves that contain only the proper six Pokemon in the first two boxes, but the rest of the boxes contain random Pokemon, then I open the SAME three saves (empty, full1, full2), decryption is not fully successful. When I re-open empty, a single ~ marked Pokemon appears. When I re-open full1 or full2, only 929 Pokemon appear, and the slot that does not appear matches the slot that appeared in empty with the ~ marker.
Is there a way to ignore all other boxes in the initial decryption so subsequent decryptions are fully successful, regardless of the state of other boxes in the initial decryption saves?